genome.fa.s4.2.7.7.80.10.50.1000.4.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: chr4
Parameters: 2 7 7 80 10 50 1000
Length:  31929104

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   

This is table  4  of  82  ( 9773 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1015404--1016562	579	2.0	579	92	0	1924	18	25	15	40	1.90
1035288--1035376	26	3.3	27	82	4	108	50	8	7	32	1.63
1035380--1035718	116	2.9	117	75	9	325	45	11	12	30	1.78
1035384--1035708	117	2.8	113	76	8	305	45	11	12	29	1.77
1035599--1035807	100	2.1	98	79	6	226	45	11	12	30	1.78
1039734--1039763	10	3.0	10	90	0	51	66	0	0	33	0.92
1042336--1042653	161	2.0	161	94	0	555	28	13	24	34	1.93
1047394--1047467	30	2.5	30	82	4	89	62	0	1	36	1.04
1047408--1047452	22	2.1	22	84	12	58	66	0	0	33	0.92
1052447--1052521	34	2.2	34	83	4	98	66	0	0	33	0.92
1066288--1066344	26	2.2	26	87	3	80	52	8	8	29	1.62
1066286--1066345	25	2.4	25	81	8	77	50	8	8	33	1.63
1066644--1066686	19	2.2	20	91	4	70	30	16	18	34	1.93
1066772--1066850	28	2.9	27	77	3	88	46	10	10	32	1.71
1074524--1074557	11	3.1	11	86	0	50	26	11	20	41	1.87
1086719--1086749	2	15.5	2	100	0	62	48	0	0	51	1.00
1091276--1091740	90	5.2	90	72	5	330	26	15	31	27	1.95
1091330--1091712	180	2.1	180	83	1	482	25	17	30	26	1.97
1092158--1092185	3	9.3	3	100	0	56	32	0	0	67	0.91
1092302--1092383	25	3.2	24	71	25	62	48	1	2	47	1.22
1092781--1092825	23	1.9	24	86	4	65	48	2	4	44	1.35
1092888--1092925	17	2.3	17	90	4	60	26	0	0	73	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1107520--1107559	20	2.1	19	90	9	64	57	0	0	42	0.98
1107556--1107595	17	2.4	17	83	8	55	30	2	0	67	1.04
1115128--1115167	20	2.0	20	90	9	64	52	0	0	47	1.00
1130921--1130954	11	3.0	11	83	8	50	8	5	2	82	0.93
1133343--1133738	199	2.0	196	97	2	749	40	16	10	32	1.82
1135186--1135245	24	2.5	24	94	0	102	26	15	31	26	1.95
1135131--1135263	24	5.8	24	72	11	98	27	10	33	28	1.90
1135350--1135431	24	3.5	24	66	15	71	28	21	26	23	1.99
1135302--1135595	47	6.3	47	79	1	293	28	21	27	22	1.99
1135345--1135621	141	2.0	141	82	1	340	28	20	26	24	1.99
1136253--1136858	31	19.5	31	88	1	829	26	17	18	38	1.92
1138226--1138578	145	2.4	145	79	3	363	30	20	18	30	1.96
1140651--1140878	118	1.9	117	85	0	312	28	26	19	25	1.99
1145574--1145606	2	17.0	2	93	6	59	48	0	0	51	1.00
1149078--1149149	32	2.4	31	86	6	94	33	15	13	37	1.87
1149172--1149229	30	1.9	30	85	0	80	31	15	13	39	1.86
1149241--1149316	24	3.2	24	92	0	107	21	17	22	39	1.92
1152650--1152695	23	2.0	24	91	4	76	43	2	28	26	1.66
1152650--1152698	12	4.2	12	89	2	73	40	2	26	30	1.67
1152854--1153051	24	8.2	24	80	6	211	41	21	17	19	1.90
1153063--1153157	29	3.3	29	84	8	106	42	15	10	31	1.81
1154787--1154822	2	18.5	2	94	5	65	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1154797--1154879	43	1.9	43	97	2	150	42	7	6	43	1.57
1155400--1155457	20	2.8	21	79	10	57	44	15	0	39	1.47
1155611--1155653	4	10.5	4	80	5	50	48	6	2	41	1.43
1164595--1164730	64	2.1	66	83	5	170	3	25	9	61	1.43
1166309--1166440	42	3.1	41	80	8	149	25	21	30	22	1.99
1166338--1166463	42	3.0	41	81	2	126	26	21	30	21	1.98
1166503--1166530	2	14.0	2	100	0	56	50	0	0	50	1.00
1166786--1166827	21	2.0	21	90	0	66	40	21	21	16	1.91
1168882--1169068	36	5.2	36	83	1	225	44	14	5	34	1.68
1168882--1169068	71	2.6	72	86	1	252	44	14	5	34	1.68
1175723--1175778	29	1.9	29	92	0	94	44	7	30	17	1.76
1175717--1175786	29	2.4	28	81	9	86	44	8	27	20	1.80
1176066--1176140	26	2.9	26	95	0	132	18	22	22	36	1.95
1176111--1176184	35	2.1	35	89	0	112	18	20	18	41	1.90
1177373--1177441	35	2.0	35	97	0	129	30	17	18	33	1.94
1180891--1180962	2	36.0	2	86	5	101	0	51	2	45	1.15
1182358--1182410	25	2.1	26	82	3	63	52	1	0	45	1.11
1184073--1184104	14	2.2	15	94	5	57	68	6	0	25	1.12
1188735--1188787	24	2.2	24	86	3	72	33	1	9	54	1.43
1188745--1188794	24	2.1	24	100	0	100	32	4	4	60	1.34
1190338--1190386	2	24.5	2	100	0	98	0	48	0	51	1.00
1197037--1197106	25	2.8	24	80	6	86	45	2	4	47	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1198229--1198259	3	10.3	3	100	0	62	0	0	32	67	0.91
1202749--1202799	25	2.0	27	92	7	88	58	0	0	41	0.98
1202851--1202935	25	3.8	22	76	12	68	56	4	1	37	1.28
1202777--1203127	110	3.1	110	82	9	367	56	3	0	39	1.22
1202959--1203006	20	2.6	17	77	9	51	68	2	0	29	1.01
1202759--1203127	113	3.3	111	80	12	400	56	3	0	39	1.22
1202970--1203311	183	1.9	184	86	6	498	56	2	0	39	1.19
1203128--1203246	45	2.6	45	78	11	116	56	2	0	39	1.19
1205570--1205611	1	42.0	1	90	0	66	2	0	95	2	0.32
1219261--1219292	3	10.7	3	93	0	55	31	0	3	65	1.08
1222199--1222252	26	2.0	29	82	10	69	61	1	5	31	1.30
1223315--1223363	25	2.0	25	88	8	73	28	4	2	65	1.22
1223316--1223371	25	2.2	26	84	6	71	33	3	3	58	1.32
1227728--1227797	32	2.1	33	84	10	90	30	5	0	64	1.17
1232136--1232166	2	15.5	2	100	0	62	48	0	0	51	1.00
1242498--1242528	1	31.0	1	100	0	62	0	0	0	100	0.00
1247751--1247784	4	8.5	4	93	0	59	50	26	0	23	1.50
1251533--1251654	62	2.0	62	85	3	165	47	4	13	33	1.65
1267760--1267815	29	1.9	29	82	7	69	26	10	10	51	1.69
1267961--1268024	33	1.9	33	83	0	83	39	15	3	42	1.63
1274123--1274155	12	2.6	13	90	9	59	36	0	24	39	1.56
1280363--1280388	13	2.0	13	100	0	52	38	0	38	23	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1285396--1285484	44	2.0	44	85	8	119	33	16	22	26	1.96
1293879--1293920	17	2.6	16	78	14	50	42	0	0	57	0.99
1294224--1294256	16	2.1	16	100	0	66	33	6	30	30	1.82
1299031--1299077	24	2.0	24	100	0	94	25	25	27	21	1.99
1299094--1299176	27	3.1	27	92	0	139	34	39	7	18	1.78
1301052--1301160	54	2.0	54	89	0	164	29	31	11	28	1.91
1304535--1304567	16	2.0	17	94	5	59	72	0	0	27	0.85
1327420--1327451	2	16.0	2	100	0	64	50	0	0	50	1.00
1328221--1328257	2	18.5	2	100	0	74	48	0	51	0	1.00
1331294--1331329	2	18.0	2	100	0	72	50	0	0	50	1.00
1333225--1333406	98	1.9	94	94	3	310	45	4	8	40	1.57
1333515--1333566	24	2.3	22	77	9	59	48	1	0	50	1.12
1333529--1333574	17	2.8	18	75	24	57	47	2	0	50	1.13
1334063--1334087	6	4.2	6	100	0	50	16	0	48	36	1.46
1344914--1344980	29	2.3	29	94	0	116	44	20	8	25	1.80
1345861--1345916	29	1.9	29	82	7	69	44	0	17	37	1.49
1347260--1347296	19	1.9	19	89	10	58	37	2	2	56	1.28
1347283--1347326	21	2.1	21	83	8	54	47	0	4	47	1.22
1357319--1357380	30	2.1	30	81	6	72	17	37	20	24	1.94
1376284--1376314	15	2.1	15	93	0	53	45	0	0	54	0.99
1383681--1383721	17	2.5	17	77	18	50	65	0	0	34	0.93
1386798--1386839	16	2.5	17	92	7	68	35	4	2	57	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1388971--1389004	17	1.9	18	88	5	52	88	0	8	2	0.62
1395182--1395324	70	2.0	70	94	0	250	40	10	6	41	1.66
1398367--1398404	3	12.7	3	94	0	67	65	2	0	31	1.06
1399066--1399132	32	2.1	33	85	2	91	41	1	5	50	1.36
1399105--1399179	25	3.0	24	73	9	69	54	1	4	40	1.27
1399169--1399224	25	2.2	25	84	6	69	50	5	0	44	1.25
1400240--1400313	26	3.1	22	72	16	58	47	0	2	50	1.15
1412385--1412428	17	2.6	17	85	0	61	61	6	0	31	1.22
1415723--1415760	2	19.0	2	100	0	76	50	0	0	50	1.00
1418775--1418802	3	9.3	3	100	0	56	0	35	0	64	0.94

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82